.hack//Roots is the prequel to the .hack//G.U. videogames. It follows the story of Haseo, a black 'Adept Rogue' (a class that can use multiple weapons) and member of the Twilight Brigade guild. In the year 2015, CC Corp. Building burnt down, and with it, most of its data for The World. By splicing data from what would have potentially been another game, CC Corp. created The World R:2 and released it in 2016. The main revisions of this release were that the game allowed for guild and PvP (player vs player) play.

Starting eight months before .hack//G.U. and finishing during the events of the first .hack//G.U. game, Rebirth, Haseo logs into The World R:2 for the first time and falls victim to the PKers that reside within. He is saved by Ovan, which prompts him to join the Twilight Brigade.

The Twilight Brigade members are on a mission to find the Key of the Twilight, however, the TAN guild opposes this because they want Ovan's character data possibly because of his device in his arm and will stop at nothing to keep the Twilight Brigade from their goal.

Their current mission is to find the 6 virus cores before TAN does. Haseo has the green virus core and the purple core, Shino has the red, Sakisaka the Yellow, Ovan the grey, and Gord has the blue one. There is a Lost Ground with 5 towers, where the Brigade used the supposedly-unusable virus cores. When the five are used it transports them to the tower above the 5 small towers to where they can find the last virus core.

This mission, unfortunately, was just a trap made by the members of TAN in order to investigate Ovan's strange character data. With Ovan gone, and no sign of the Key of the Twilight, the Twilight Brigade quickly breaks apart. B-set and Gord quit the game entirely, and Sakisaka and Tabby quit the guild, even though Tabby is still hopeful things will pick up. Shino goes into 'mourning' over Ovan, as it has been hinted that their relationship is that of more than friends, with Haseo by her side supporting her. However, even this is quickly shattered, as Shino is soon after killed within the game. What's even more alarming is that Haseo can't contact her in real life.

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